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Increase max allowed compute PLs for an allele

When running GenotypeGVCFs (v3.7), I get a small number of sites (<100) that are not called because of:
DEBUG 13:35:31,518 ReferenceConfidenceVariantContextMerger - location chr21:44483184 has too many alleles (73) to compute PLs (maximum allowed 50). PL genotype annotations won't be produced at this site
WARN 13:35:31,550 GenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr21:44483184

How do I increase this number? I have played around with --max_alternate_alleles, --max_genotype_count, and --max_num_PL_values with no luck.

Best Answer

Those three parameters should be the only ones you need to raise the limit you're dealing with. Can you post what you tried and whether the results changed at all? Keep in mind that these parameters have interactions, so you typically need to raise all of them to make a difference. Be aware also that this sounds like a very messy region that will most probably not produce sensible calls anyway.

Answers

Those three parameters should be the only ones you need to raise the limit you're dealing with. Can you post what you tried and whether the results changed at all? Keep in mind that these parameters have interactions, so you typically need to raise all of them to make a difference. Be aware also that this sounds like a very messy region that will most probably not produce sensible calls anyway.